def test_cit_magic_fail_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4'
program_ran, error_message = cit_magic.main(False, **options)
self.assertFalse(program_ran)
self.assertEqual(error_message, "naming convention option [4] must be in form 4-Z where Z is an integer")
def test_cit_magic_with_file(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
program_ran, outfile = cit_magic.main(False, **options)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'magic_measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_with_file(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
program_ran, outfile = cit_magic.main(False, **options)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'magic_measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_succeed_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'pmagpy_data_files',
'Measurement_Import',
'cit_magic', 'MP18')
options['magfile'] = 'bMP.sam'
options['samp_con'] = '4-3'
program_ran, outfile = cit_magic.main(False, **options)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'magic_measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_fail_option4(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '4'
program_ran, error_message = cit_magic.main(False, **options)
self.assertFalse(program_ran)
self.assertEqual(
error_message,
"naming convention option [4] must be in form 4-Z where Z is an integer"
)
def test_cit_magic_with_other_data(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '1'
options['methods'] = ['SO-SM:SO-MAG']
options['locname'] = 'location'
options['avg'] = 1
options['specnum'] = 2
program_ran, outfile = cit_magic.main(False, **options)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'magic_measurements.txt')
self.assertEqual(outfile, expected_file)
def test_cit_magic_with_other_data(self):
options = {}
options['input_dir_path'] = os.path.join(WD, 'data_files',
'Measurement_Import',
'cit_magic', 'PI47')
options['magfile'] = 'PI47-.sam'
options['samp_con'] = '1'
options['methods'] = ['SO-SM:SO-MAG']
options['locname'] = 'location'
options['avg'] = 1
options['specnum'] = 2
program_ran, outfile = cit_magic.main(False, **options)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'magic_measurements.txt')
self.assertEqual(outfile, expected_file)
def read_inp(WD, inp_file_name, magic_files):
inp_file = open(inp_file_name, "r")
new_inp_file = ""
if type(magic_files) != dict:
magic_files = {}
if "measurements" not in magic_files.keys():
magic_files["measurements"] = []
if "specimens" not in magic_files.keys():
magic_files["specimens"] = []
if "samples" not in magic_files.keys():
magic_files["samples"] = []
if "sites" not in magic_files.keys():
magic_files["sites"] = []
lines = inp_file.read().split("\n")
if len(lines) < 3:
print(".inp file improperly formated")
return
new_inp_file = lines[0] + "\n" + lines[1] + "\n"
[lines.remove("") for i in range(lines.count(""))]
format = lines[0].strip()
header = lines[1].split("\t")
update_files = lines[2:]
update_data = False
for i, update_file in enumerate(update_files):
update_lines = update_file.split("\t")
if not os.path.isfile(update_lines[0]):
print("%s not found searching for location of file" % (update_lines[0]))
sam_file_name = os.path.split(update_lines[0])[-1]
new_file_path = find_file(sam_file_name, WD)
if new_file_path == None or not os.path.isfile(new_file_path):
print("%s does not exist in any subdirectory of %s and will be skipped" % (update_lines[0], WD))
new_inp_file += update_file + "\n"
continue
else:
print("new location for file found at %s" % (new_file_path))
update_lines[0] = new_file_path
d = os.path.dirname(update_lines[0])
name = os.path.basename(os.path.splitext(update_lines[0])[0])
erspecf = name + "_er_specimens.txt"
ersampf = name + "_er_samples.txt"
ersitef = name + "_er_sites.txt"
f = name + ".magic"
if os.path.join(d, f) in magic_files:
new_inp_file += update_file + "\n"
continue
if float(update_lines[-1]) >= os.path.getmtime(update_lines[0]):
no_changes = True
# check specimen files for changes
sam_file = open(update_lines[0])
sam_file_lines = sam_file.readlines()
spec_file_paths = map(lambda x: os.path.join(d, x.strip("\r \n")), sam_file_lines[2:])
for spec_file_path in spec_file_paths:
if float(update_lines[-1]) < os.path.getmtime(spec_file_path):
no_changes = False
break
if (
no_changes
and os.path.isfile(os.path.join(WD, f))
and os.path.isfile(os.path.join(WD, erspecf))
and os.path.isfile(os.path.join(WD, ersampf))
and os.path.isfile(os.path.join(WD, ersitef))
):
magic_files["measurements"].append(os.path.join(WD, f))
magic_files["specimens"].append(os.path.join(WD, erspecf))
magic_files["samples"].append(os.path.join(WD, ersampf))
magic_files["sites"].append(os.path.join(WD, ersitef))
new_inp_file += update_file + "\n"
continue
if len(header) != len(update_lines):
print(
"length of header and length of enteries for the file %s are different and will be skipped"
% (update_lines[0])
)
new_inp_file += update_file + "\n"
continue
update_dict = {}
for head, entry in zip(header, update_lines):
update_dict[head] = entry
if format == "CIT":
CIT_kwargs = {}
CIT_name = os.path.basename(os.path.splitext(update_dict["sam_path"])[0])
CIT_kwargs["dir_path"] = WD # reduce(lambda x,y: x+"/"+y, update_dict["sam_path"].split("/")[:-1])
CIT_kwargs["user"] = ""
CIT_kwargs["meas_file"] = CIT_name + ".magic"
CIT_kwargs["spec_file"] = CIT_name + "_er_specimens.txt"
CIT_kwargs["samp_file"] = CIT_name + "_er_samples.txt"
CIT_kwargs["site_file"] = CIT_name + "_er_sites.txt"
CIT_kwargs["locname"] = update_dict["location"]
CIT_kwargs["methods"] = update_dict["field_magic_codes"]
CIT_kwargs["specnum"] = update_dict["num_terminal_char"]
CIT_kwargs["avg"] = update_dict["dont_average_replicate_measurements"]
CIT_kwargs["samp_con"] = update_dict["naming_convention"]
CIT_kwargs["peak_AF"] = update_dict["peak_AF"]
CIT_kwargs["magfile"] = os.path.basename(update_dict["sam_path"])
CIT_kwargs["input_dir_path"] = os.path.dirname(update_dict["sam_path"])
program_ran, error_message = cit_magic.main(command_line=False, **CIT_kwargs)
measp = os.path.join(CIT_kwargs["dir_path"], CIT_kwargs["meas_file"])
specp = os.path.join(CIT_kwargs["dir_path"], CIT_kwargs["spec_file"])
sampp = os.path.join(CIT_kwargs["dir_path"], CIT_kwargs["samp_file"])
sitep = os.path.join(CIT_kwargs["dir_path"], CIT_kwargs["site_file"])
if program_ran:
update_data = True
update_lines[-1] = time()
new_inp_file += reduce(lambda x, y: str(x) + "\t" + str(y), update_lines) + "\n"
magic_files["measurements"].append(measp)
magic_files["specimens"].append(specp)
magic_files["samples"].append(sampp)
magic_files["sites"].append(sitep)
else:
new_inp_file += update_file
if os.path.isfile(measp) and os.path.isfile(specp) and os.path.isfile(sampp) and os.path.isfile(sitep):
magic_files["measurements"].append(measp)
magic_files["specimens"].append(specp)
magic_files["samples"].append(sampp)
magic_files["sites"].append(sitep)
inp_file.close()
out_file = open(inp_file_name, "w")
out_file.write(new_inp_file)
return update_data
def test_cit_with_no_files(self):
program_ran, error_message = cit_magic.main(False)
self.assertFalse(program_ran)
self.assertEqual(error_message, 'bad sam file name')
def test_cit_with_no_files(self):
program_ran, error_message = cit_magic.main(False)
self.assertFalse(program_ran)
self.assertEqual(error_message, 'bad sam file name')
